Good practice

• Organize your folders carefully, and name them meaningfully:
  • /User/czmann/Stat331/lab1/ rather than Desktop/stuff/
• In general, use R Projects liberally - put one in the “main” folder for a project

Bad practice

If you put something like this at the top of your .qmd file (more on Quarto later), I will set your computer on fire:

setwd("/User/chappelroan/Desktop/R_Class/Lab_1/")

• Setting working directory by hand = BAD!

Scripts

• Scripts (File > New File > R Script) are files of code that are meant to be run on their own.

Notebooks

Notebooks are an implementation of literate programming.

• They allow you to integrate code, output, text, images, etc. into a single document.

• E.g.,

  • R Markdown notebook
  • Quarto notebook
  • Jupyter notebook

Reproducibility!

What is Markdown?

Markdown (without the “R”) is a markup language.

• It uses special symbols and formatting to make pretty documents.

• Markdown files have the .md extension.

What is R Markdown?

R Markdown (with the “R”) uses regular Markdown, AND it can run and display R code.

• (Other languages, too!)
• R Markdown files have the .Rmd extension.

What is Quarto?

Quarto unifies and extends the R Markdown ecosystem.

• Quarto files have the .qmd extension.

Quarto is the next generation R Markdown.

Highlights of Quarto

• Consistent implementation of attractive and handy features across outputs:

  • E.g., tabsets, code-folding, syntax highlighting, etc.

• More accessible defaults and better support for accessibility.

• Guardrails that are helpful when learning:

  • E.g., YAML completion, informative syntax errors, etc.

• Support for other languages like Python, Julia, Observable, and more.

Quarto Formats

Quarto makes moving between outputs straightforward.

• All that needs to change between these formats is a few lines in the front matter (YAML)!

title: "Lesson 1"
format: html

title: "Lesson 1"
format: revealjs

project:
  type: website

website: 
  navbar: 
    left:
      - lesson-1.qmd

Quarto Components

Markdown in Quarto

A few useful tips for formatting the Markdown text in your document:

• *text* – makes italics
• **text** – makes bold text
• # – makes headers
•  – includes images or HTML links
• < > – embeds URLs

R Code Options in Quarto

R code chunk options are included at the top of each code chunk, prefaced with a #| (hashpipe).

• These options control how the following code is run and reported in the final Quarto document.
• R code options can also be included in the front matter (YAML) and are applied globally to the document.

Rendering your Quarto Document

To take your .qmd file and make it look pretty, you have to render it.

Rendering your Quarto Document

Quarto CLI (command line interface) orchestrates each step of rendering:

1. Process the executable code chunks with either knitr or jupyter.
2. Convert the resulting Markdown file to the desired output.

Rendering your Quarto Document

When you click Render:

• Your file is saved.
• The R code written in your .qmd file gets run in order.
  • It starts from scratch, even if you previously ran some of the code.
• A new file is created.
  • If your Quarto file is called “Lab1.qmd”, then a file called “Lab1.html” will be created.
  • This will be saved in the same folder as “Lab1.qmd”.

Lab 1: Introduction to Quarto + Challenge 1: Modifying your Quarto Document

To do…

• Lab 1: Introduction to Quarto
  • Due Saturday (1/11) at 11:59pm
• Read Chapter 2: Importing Data + Basics of Graphics
  • Check-in 2.1 + 2.2 due Monday (1/13 at 10:00am